logLikExtHyp

This function calculates the logarithm of the Extended Hypergeometric likelihood at specified x and alpha, with marginal totals mA, mB, N fixed.

Computes a novel metric of affinity between two entities based on their co-occurrence
(using binary presence/absence data). The metric and its MLE, alpha hat, were advanced in
Mainali, Slud, et al, 2021 <doi:10.1126/sciadv.abj9204>. Various types of confidence intervals and median interval
were developed in Mainali and Slud, 2022 <doi:10.1101/2022.11.01.514801>.

Kumar Mainali

CooccurrenceAffinity

Affinity in Co-Occurrence Data

Eric Slud

logLikExtHyp function

<dl><dt>x</dt>
<dd>integer co-occurrence count that should properly fall within the closed interval [max(0,mA+mB-N), min(mA,mB)]</dd>
<dt>marg</dt>
<dd>a 3-entry integer vector (mA,mB,N) consisting of the first row and column totals and the table total for a 2x2 contingency table</dd>
<dt>alpha</dt>
<dd>a real number, the log odds ratio or affinity parameter for the 2x2 contingency table</dd></dl>

Arguments

Author

log of Extended Hypergeometric Likelihiood at (X, mA,mB,N, alpha) — logLikExtHyp

<dl>

<dt>x</dt>
<dd>integer co-occurrence count that should properly fall within the closed interval [max(0,mA+mB-N), min(mA,mB)]</dd>


<dt>marg</dt>
<dd>a 3-entry integer vector (mA,mB,N) consisting of the first row and column totals and the table total for a 2x2 contingency table</dd>


<dt>alpha</dt>
<dd>a real number, the log odds ratio or affinity parameter for the 2x2 contingency table</dd>

</dl>

logLikExtHyp: log of Extended Hypergeometric Likelihiood at (X, mA,mB,N, alpha)

Description

Usage

Value

Arguments

Author

Details

References

Examples